org.forester.msa_compactor

Class MsaCompactor

java.lang.Object

org.forester.msa_compactor.MsaCompactor

public class MsaCompactor
extends Object

Constructor Summary

Constructors

Constructor and Description
MsaCompactor(DeleteableMsa msa)

Method Summary

Modifier and Type	Method and Description
Phylogeny	calcTree()
List<MsaProperties>	chart(int step, boolean realign, boolean normalize_for_effective_seq_length)
void	deleteGapColumns(double max_allowed_gap_ratio)
void	displayTree(Phylogeny phy)
Msa	getMsa()
static String	guessPathToMafft()
void	removeSequencesByMinimalLength(int min_effective_length)
List<MsaProperties>	removeViaGapAverage(double mean_gapiness)
List<MsaProperties>	removeViaLength(int length)
List<MsaProperties>	removeWorstOffenders(int to_remove)
void	setCalculateNormalizedShannonEntropy(boolean calculate_shannon_entropy)
void	setInfileName(String infile_name)
void	setMafftOptions(String maffts_opts)
void	setNorm(boolean normalize_for_effective_seq_length)
void	setOutFileBase(File out_file_base)
void	setOutputFormat(Msa.MSA_FORMAT output_format)
void	setPathToMafft(String path_to_mafft)
void	setPeformPhylogenticInference(boolean phylogentic_inference)
void	setRealign(boolean realign)
void	setRemovedSeqsOutBase(File removed_seqs_out_base)
void	setStep(int step)
void	setStepForDiagnostics(int step_for_diagnostics)
String	writeAndAlignRemovedSeqs()
String	writeMsa(File outfile)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MsaCompactor

public MsaCompactor(DeleteableMsa msa)

Method Detail

calcTree

public final Phylogeny calcTree()

chart

public final List<MsaProperties> chart(int step,
                                       boolean realign,
                                       boolean normalize_for_effective_seq_length)
                                throws IOException,
                                       InterruptedException

Throws:

IOException

InterruptedException

deleteGapColumns

public final void deleteGapColumns(double max_allowed_gap_ratio)

displayTree

public final void displayTree(Phylogeny phy)

getMsa

public final Msa getMsa()

removeSequencesByMinimalLength

public final void removeSequencesByMinimalLength(int min_effective_length)
                                          throws IOException

Throws:

IOException

removeViaGapAverage

public final List<MsaProperties> removeViaGapAverage(double mean_gapiness)
                                              throws IOException,
                                                     InterruptedException

Throws:

IOException

InterruptedException

removeViaLength

public List<MsaProperties> removeViaLength(int length)
                                    throws IOException,
                                           InterruptedException

Throws:

IOException

InterruptedException

removeWorstOffenders

public final List<MsaProperties> removeWorstOffenders(int to_remove)
                                               throws IOException,
                                                      InterruptedException

Throws:

IOException

InterruptedException

setCalculateNormalizedShannonEntropy

public final void setCalculateNormalizedShannonEntropy(boolean calculate_shannon_entropy)

setInfileName

public void setInfileName(String infile_name)

setMafftOptions

public final void setMafftOptions(String maffts_opts)

setNorm

public final void setNorm(boolean normalize_for_effective_seq_length)

setOutFileBase

public final void setOutFileBase(File out_file_base)

setOutputFormat

public final void setOutputFormat(Msa.MSA_FORMAT output_format)

setPathToMafft

public void setPathToMafft(String path_to_mafft)

setPeformPhylogenticInference

public void setPeformPhylogenticInference(boolean phylogentic_inference)

setRealign

public final void setRealign(boolean realign)

setRemovedSeqsOutBase

public final void setRemovedSeqsOutBase(File removed_seqs_out_base)

setStep

public final void setStep(int step)

setStepForDiagnostics

public final void setStepForDiagnostics(int step_for_diagnostics)

writeAndAlignRemovedSeqs

public final String writeAndAlignRemovedSeqs()
                                      throws IOException,
                                             InterruptedException

Throws:

IOException

InterruptedException

writeMsa

public final String writeMsa(File outfile)
                      throws IOException

Throws:

IOException

guessPathToMafft

public static final String guessPathToMafft()